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Coexpression cluster:C1871: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;2.24383,MA0004.1;0.626788,MA0006.1;2.00428,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.660087,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;4.94778,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.554727,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;1.55172,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.362215,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.412364,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;1.96988,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.973423,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.946108,MA0147.1;2.66688,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;2.38271,MA0138.2;0.837782,MA0002.2;3.17169,MA0137.2;0.47779,MA0104.2;2.35335,MA0047.2;0.767096,MA0112.2;0.839774,MA0065.2;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;5.73519,MA0163.1;1.99104,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;3.54347,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;1.02361,MA0442.1;0
}}
}}

Revision as of 20:15, 22 January 2013


Full id: C1871_breast_MCF7_clear_renal_amniotic_leiomyoblastoma_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr20:49347993..49348004,+p7@PARD6B
Hg19::chr20:49348006..49348019,+p5@PARD6B
Hg19::chr20:49348020..49348069,+p2@PARD6B
Hg19::chr20:49348083..49348096,+p3@PARD6B
Hg19::chr20:49367522..49367525,+p@chr20:49367522..49367525
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell7.33e-20253
endodermal cell3.98e-1058
Uber Anatomy
Ontology termp-valuen
trunk region element1.30e-13101
digestive system3.49e-10145
digestive tract3.49e-10145
primitive gut3.49e-10145
endo-epithelium4.45e-1082
endoderm-derived structure9.31e-10160
endoderm9.31e-10160
presumptive endoderm9.31e-10160
subdivision of digestive tract1.25e-09118
abdomen element5.69e-0954
abdominal segment element5.69e-0954
subdivision of trunk9.87e-08112
organ system subdivision2.13e-07223
kidney2.30e-0726
kidney mesenchyme2.30e-0726
upper urinary tract2.30e-0726
kidney rudiment2.30e-0726
kidney field2.30e-0726
cavitated compound organ3.12e-0731
abdominal segment of trunk8.35e-0760
abdomen8.35e-0760
renal system8.46e-0748
immaterial anatomical entity8.92e-07117


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.24383
MA0004.10.626788
MA0006.12.00428
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.14.94778
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.362215
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.96988
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.946108
MA0147.12.66688
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.38271
MA0138.20.837782
MA0002.23.17169
MA0137.20.47779
MA0104.22.35335
MA0047.20.767096
MA0112.20.839774
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.15.73519
MA0163.11.99104
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.54347
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BHLHE40#8553217.9487254187910.004747812859838950.0223188021455966
CCNT2#90545.068961261570110.002709998091280770.0148994257030571
CEBPB#105146.376918100659850.001113944176677320.00765641433813769
CHD2#110648.275218267293490.0004028373567101730.00387866974255128
E2F1#186943.925911371903460.007214984547106360.0298792882792831
E2F6#187644.013724585357910.006632118233933880.0283015361703776
EGR1#195843.990543275848110.0067800983001440.0287696211907829
FOS#235347.198364247115530.0006947858453382510.00559811286076852
HDAC2#3066410.7324961893010.0001450965797478750.00188643616236627
HMGN3#932446.542838178680470.00100801277768350.00722155621405455
IRF1#365946.109731002851120.001315525264767990.00881170748634585
MAX#414945.16204440720570.002526309009485180.0140008058711394
MXI1#460147.969257303007440.0004668546380070170.00429584418844184
NFKB1#479044.390450739355070.004707732692524960.0222083605706949
NFYB#4801413.40783460282926.03169250119439e-050.000991725335535643
NRF1#489949.768223558168730.0002101297748106790.00244548067210302
RFX5#599349.638328661756080.000221480125815720.0024976960220352
SIN3A#2594244.327107781452110.004977052855762880.0232478385975678
SP1#666744.558705102512720.00407573565781680.01948929794271
SP2#6668420.92282439507571.03516506540382e-050.000269470598867671
TAF7#687949.146455523939130.0002720662872412990.00290327280813263
TCF12#693848.507571921749140.0003614215578492260.0036124515341387
USF1#739145.089199421766370.00266867775360040.0147210709295026
USF2#7392410.39375790805570.0001646179728687530.00202694370059417
ZEB1#6935413.51074561403515.85221769500384e-050.00096708823393751



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1871&oldid=2570382"